[CP2K:2142] Cell size problem

Laino Teodoro teodor... at gmail.com
Thu Jun 25 21:25:03 UTC 2009


Very probably it is an allocation problem (running out of memory).
To be sure you should post more info. For example, in the working   
directory there should be
several *localLog* files. The content of one of them would be helpful..

Teo

On 25 Jun 2009, at 22:49, roberto wrote:

>
> I have perfomed a WF optimization of a little peptide in vacuo without
> problem.
> If I try to increase the size of the cell (from 35x35x35 to 40x40x40),
> the simulation fail.
> I post the inputfile and follow the output error message.
>
> Thanks for any suggestion.
>
>
> ## INPUT ##
> &FORCE_EVAL
>   METHOD Quickstep
>   &DFT
>     &POISSON
>       PERIODIC NONE
>       POISSON_SOLVER MT
>     &END POISSON
>     CHARGE +1
>     &MGRID
>       CUTOFF 280
>     &END MGRID
>     &QS
>       EPS_DEFAULT 1.0E-8
>     &END QS
>     &SCF
>       &OT
>         PRECONDITIONER FULL_SINGLE_INVERSE
>       &END OT
>       MAX_SCF 40
>       &OUTER_SCF
>         MAX_SCF 5
>       &END OUTER_SCF
>   &END SCF
>     &XC
>       &XC_FUNCTIONAL BLYP
>       &END XC_FUNCTIONAL
>     &END XC
>   &END DFT
>   &SUBSYS
>     &CELL
>       PERIODIC NONE
>       ABC 40.0 40.0 40.0
>       UNIT ANGSTROM
>     &END CELL
>     &COORD
>   N        11.4324736309       -6.1371572063       10.1357218931
>   H        11.1948075937       -6.8906101345       10.7821924672
>   H        10.9381862969       -6.3405541515        9.2632495044
>   C        10.9499715702       -4.8402675750       10.6521973274
>   H        11.3386245365       -4.7296425589       11.6677585473
>   C        11.4913131810       -3.6752836914        9.7832152944
>   H        11.2516744925       -3.8960378486        8.7344971467
>   H        10.9285010983       -2.7702123308       10.0417793494
>   C        12.9962124352       -3.4081941284        9.9438576821
>   H        13.2545611858       -3.3414422460       11.0083607468
>   H        13.5793843176       -4.2349628942        9.5244606629
>   C        13.4276150724       -2.0986464686        9.2465939026
>   H        14.5097616796       -1.9519749811        9.3487493765
>   H        13.1879571320       -2.1284201500        8.1783151066
>   N        12.7146699325       -0.9515928240        9.8558121776
>   H        12.5828552979       -1.0107633654       10.8919178425
>   C        12.1135559906        0.0441274020        9.2139901029
>   N        12.4394518112        0.3403191250        7.9167217260
>   H        13.4354822732        0.3681036873        7.7191911152
>   H        11.9329746051        1.1211570509        7.5131991344
>   N        11.1218376294        0.7371180721        9.8136134969
>   H        10.8845997299        0.4742930918       10.7753580754
>   H        11.0626157210        1.7370925590        9.6197738858
>   C         9.4085853225       -4.6963484515       10.6225043190
>   O         8.7929578553       -4.9975325132        9.5903800315
>   N         8.7856778560       -4.1441412798       11.7203597433
>   C         7.3486285567       -3.8102551517       11.7099480717
>   H         6.8197192907       -4.5278210668       11.0766326891
>   C         6.9582417964       -3.9259460918       13.2069269204
>   H         6.0748168733       -3.3358993177       13.4681026699
>   H         6.7441098192       -4.9759288944       13.4343207792
>   C         8.2282987207       -3.4419031893       13.9424055935
>   H         8.2310874957       -2.3492127686       13.9975911707
>   H         8.2955580201       -3.8288025246       14.9625954573
>   C         9.4034512549       -3.9235517293       13.0609426956
>   H        10.2003124860       -3.1759063533       13.0064126519
>   H         9.8280374116       -4.8622782613       13.4349980596
>   C         7.1101286450       -2.3801594356       11.1412507028
>   O         8.0203520380       -1.5310504742       11.0477720011
>   N         5.8392674941       -2.0823894794       10.7205335448
>   C         5.6355139703       -0.8941970496        9.8616586631
>   H         6.4068582242       -0.9016299355        9.0817309576
>   C         4.2200778144       -1.1170421588        9.2549104403
>   H         3.7003760394       -0.1719620880        9.0653987172
>   H         4.3221404500       -1.6430084891        8.2982109770
>   C         3.4941370231       -2.0064473870       10.2877472021
>   H         3.0786537890       -1.3852707278       11.0878641139
>   H         2.6836333737       -2.5921705326        9.8413944307
>   C         4.6079587796       -2.9171615522       10.8501847587
>   H         4.4363094156       -3.1758339663       11.8977183292
>   H         4.7026866900       -3.8463230114       10.2747817658
>   C         5.7458899497        0.4525397791       10.6137692543
>   O         5.2154503855        0.7039309036       11.7192531172
>   N         6.4344225918        1.3948594344        9.9368461571
>   H         6.9322429528        1.1986520759        9.0691552019
>   C         6.5700409770        2.7589843070       10.4088570300
>   H         5.5947332208        3.1651635665       10.6980024914
>   H         7.2187935767        2.8031426981       11.2970319085
>   C         7.2295977003        3.5687623281        9.2776439289
>   O         7.7340229907        2.9845949290        8.3112331112
>   N         7.2238485090        4.9191972013        9.5096174983
>   H         6.6972441974        5.2437226270       10.3188538415
>   C         7.9461520189        5.9673404267        8.7653679704
>   H         8.0948922681        5.6108506893        7.7422282223
>   C         7.1259847303        7.2983111829        8.7421278471
>   H         7.7166350535        8.0185624933        8.1702963661
>   H         6.1954232051        7.1154799216        8.1942654314
>   C         6.8262531031        7.8236225973       10.1409243252
>   C         7.8009125294        8.5254653877       10.8745041594
>   H         8.7512326191        8.7682386096       10.4069719956
>   C         5.5931262870        7.5527765173       10.7617727760
>   H         4.7994354740        7.0694296050       10.1946741872
>   C         7.5588299749        8.9164837495       12.1941172113
>   H         8.3165010987        9.4774015857       12.7357860474
>   C         5.3567146254        7.9306360270       12.0896783873
>   H         4.3996280301        7.7066013719       12.5536143802
>   C         6.3440138894        8.6051885011       12.8127723611
>   H         6.1632870999        8.8990656943       13.8430462390
>   C         9.3571813479        6.2746847214        9.3428304585
>   O        10.0791474867        7.1283336115        8.8105336198
>   N         9.6823888175        5.6087213903       10.4868666966
>   H         9.1151350681        4.8239948493       10.7846719438
>   C        11.0098655520        5.6810980820       11.0893328531
>   H        11.3426585696        6.7203820495       11.0590121012
>   C        10.9201366090        5.2066006718       12.5630668632
>   H        11.9200185517        5.1756653398       13.0151902147
>   H        10.3015773371        5.9179548033       13.1188135468
>   O        10.2584835828        3.9285493471       12.6795126544
>   H        10.8564137049        3.2408538678       12.3296344025
>   C        11.9591884550        4.7647976442       10.3069677329
>   O        11.6296147202        3.5817188030       10.0708465781
>   N        13.1788137378        5.2443511260        9.9396802843
>   C        14.0563338490        4.4032200505        9.0829530013
>   H        13.4719025368        4.0064794776        8.2494747614
>   C        15.1397054888        5.3960392482        8.5730358684
>   H        16.1203110935        4.9234846486        8.4844687895
>   H        14.8553721417        5.7493278524        7.5765557887
>   C        15.1264756032        6.5643344145        9.5850212352
>   H        15.7735259998        6.3373775806       10.4394603902
>   H        15.4728307826        7.5034783310        9.1434240480
>   C        13.6595469021        6.6572283699       10.0451222428
>   H        13.5728058669        7.0165901585       11.0727973352
>   H        13.0585342596        7.3015141176        9.3943770370
>   C        14.6014154503        3.1332153934        9.7817732244
>   O        14.7387246309        2.1025043414        9.1057259732
>   N        14.9321391220        3.2469089599       11.1089829812
>   H        14.5620137473        4.0402574483       11.6282916218
>   C        15.3192535703        2.1011402694       11.9474204093
>   H        15.0780360517        1.2020681276       11.3732515255
>   C        16.8585665040        2.0994231406       12.2382822730
>   H        17.3539614068        2.1958403990       11.2643638601
>   H        17.1082296466        2.9955427380       12.8181669038
>   C        17.3697857804        0.8568138702       12.9524885282
>   C        17.3797137994       -0.3930013796       12.3059460314
>   H        17.0418999476       -0.4717813269       11.2744331783
>   C        17.8502344440        0.9299228647       14.2688436131
>   H        17.8584539601        1.8877312361       14.7838482599
>   C        17.8431707860       -1.5357637564       12.9659077610
>   H        17.8448134688       -2.4938071540       12.4526028964
>   C        18.3280162135       -0.2086287981       14.9255393119
>   H        18.7080035730       -0.1258151027       15.9403383929
>   C        18.3199824362       -1.4468283157       14.2780028322
>   H        18.6875105233       -2.3333511257       14.7873511883
>   C        14.4291885252        2.1139040343       13.2372349862
>   O        13.8712375863        3.1460055627       13.6428990047
>   N        14.3252227703        0.8875480108       13.8432137400
>   H        14.8187807167        0.1440451701       13.3544501520
>   C        13.0771550709        0.3363039184       14.4658453947
>   H        13.4083046903       -0.5658317525       14.9919599824
>   C        12.3866081840        1.2690277101       15.4739897598
>   H        13.1573362728        1.6845612875       16.1305225542
>   H        11.9429043004        2.1192890169       14.9506741542
>   C        11.3196142795        0.5168432069       16.3320382507
>   H        11.2988399674       -0.5507043523       16.0745237971
>   H        11.5970777966        0.5648971423       17.3905058535
>   C         9.8816633280        1.0607292795       16.2237239485
>   H         9.2322412111        0.5053361766       16.9120837269
>   H         9.8604573253        2.1217563077       16.5141963374
>   N         9.3703250501        0.8983805551       14.8491982364
>   H        10.0820115597        0.7932029452       14.0786879557
>   C         8.0864971754        0.8564153995       14.5080177069
>   N         7.1078801829        1.1398390529       15.4161841516
>   H         7.3261229183        1.6921520704       16.2346043529
>   H         6.1392249660        1.1152097272       15.1215765008
>   N         7.7231598143        0.5099811222       13.2596078532
>   H         6.7554425343        0.5884413276       12.9348072587
>   H         8.3607775713        0.0058338362       12.6465521841
>   C        12.2320591043       -0.1584710118       13.2320032792
>   O        12.7682553788       -1.1027541201       12.5820166002
>   O        11.1533115804        0.4532114808       12.9004593689
>     &END COORD
>     &KIND H
>       BASIS_SET TZV2P-GTH
>       POTENTIAL GTH-BLYP-q1
>     &END KIND
>     &KIND C
>       BASIS_SET TZV2P-GTH
>       POTENTIAL GTH-BLYP-q4
>     &END KIND
>     &KIND N
>       BASIS_SET TZV2P-GTH
>       POTENTIAL GTH-BLYP-q5
>     &END KIND
>     &KIND O
>       BASIS_SET TZV2P-GTH
>       POTENTIAL GTH-BLYP-q6
>     &END KIND
>   &END SUBSYS
> &END FORCE_EVAL
>
> &MOTION
>   &GEO_OPT
>     OPTIMIZER LBFGS
>     MAX_ITER    100
>     &CG
>        MAX_STEEP_STEPS 5
>        &LINE_SEARCH
>          TYPE 2PNT
>        &END LINE_SEARCH
>     &END CG
>   &END GEO_OPT
>
>   &MD
>     ENSEMBLE NVT
>     STEPS 50000
>     TIMESTEP 1.0
>     TEMPERATURE 50.0
>   &END MD
>
>   &PRINT
>     &FORCES
>        FORMAT XMOL
>        &EACH
>           MD 1
>        &END EACH
>     &END FORCES
>   &END PRINT
> &END MOTION
>
> &GLOBAL
>   PROJECT 6
>   RUN_TYPE WFN_OPT
>   PRINT_LEVEL LOW
> &END GLOBAL
>
> ############################################
> CP2K| version string:                  CP2K version 2.0.0 (Development
> Version)
>  CP2K| is freely available from                          http:// 
> cp2k.berlios.de/
>  CP2K| Program compiled at                         Thu Apr 24 00:52:50
> CEST 2008
>  CP2K| Program compiled
> on                                              node1309
>  CP2K| Program compiled for                                   Linux-
> x86-64-intel
>  CP2K| Last CVS
> entry
>  CP2K| Input file name
> prot_6_2103.inp
>
>  GLOBAL| Force Environment
> number                                              1
>  GLOBAL| Basis set file name
> BASIS_SET
>  GLOBAL| Potential file name
> POTENTIAL
>  GLOBAL| MM Potential file name
> MM_POTENTIAL
>  GLOBAL| Coordinate file name
> __STD_INPUT__
>  GLOBAL| Method
> name                                                        CP2K
>  GLOBAL| Project
> name                                                          6
>  GLOBAL| Preferred FFT
> library                                             FFTW2
>  GLOBAL| Run
> type                                                         ENERGY
>  GLOBAL| All-to-all communication in single
> precision                          F
>  GLOBAL| FFTs using library dependent
> lengths                                  F
>  GLOBAL| Global print
> level                                                    1
>  GLOBAL| Total number of message passing
> processes                            16
>  GLOBAL| Number of threads for this
> process                                    1
>  GLOBAL| This output is from
> process                                           0
>
>
>  GENERATE|  Preliminary Number of Bonds
> generated:                             0
>  GENERATE|  Achieved consistency in connectivity generation.
>  GENERATE|  Number of Bonds
> generated:                                         0
>  GENERATE|  Preliminary Number of Bends
> generated:                             0
>  GENERATE|  Number of Bends
> generated:                                         0
>  GENERATE|  Number of UB
> generated:                                            0
>  GENERATE|  Preliminary Number of Torsions
> generated:                          0
>  GENERATE|  Number of Torsions
> generated:                                      0
>  GENERATE|  Number of Impropers
> generated:                                     0
>  GENERATE|  Number of 1-4 interactions
> generated:                              0
>
>
> ********************************************************************** 
> *********
>
> ********************************************************************** 
> *********
>
> **
> **
>  **     #####                         ##
> ##                      **
>  **    ##   ##            ##          ##
> ##                      **
>  **   ##     ##                       ##
> ######                    **
>  **   ##     ##  ##   ##  ##   #####  ##  ##   ####   ##    #####
> #####    **
>  **   ##     ##  ##   ##  ##  ##      ## ##   ##      ##   ##   ##
> ##   ##   **
>  **   ##  ## ##  ##   ##  ##  ##      ####     ###    ##   ######
> ######    **
>  **    ##  ###   ##   ##  ##  ##      ## ##      ##   ##   ##
> ##        **
>  **     #######   #####   ##   #####  ##  ##  ####    ##    #####
> ##        **
>  **           ##
> ##        **
>
> **
> **
>  **                                                ... make the atoms
> dance   **
>
> **
> **
>  **            Copyright (C) by CP2K Developers Group (2000 -
> 2008)           **
>
> **
> **
>
> ********************************************************************** 
> *********
>
>
>  SCF PARAMETERS         Density
> guess:                                    ATOMIC
>
> --------------------------------------------------------
>
> max_scf:                                              40
>
> max_scf_history:                                       0
>
> max_diis:                                              4
>
> --------------------------------------------------------
>
> eps_scf:                                        1.00E-05
>
> eps_scf_history:                                0.00E+00
>
> eps_diis:                                       1.00E-01
>
> eps_eigval:                                     1.00E-05
>
> eps_jacobi:                                     0.00E+00
>
> jacobi_threshold:                               1.00E-07
>
> --------------------------------------------------------
>
> p_mix:                                              0.40
>                         G-space mixing
> a:                                   1.00
>                         G-space mixing
> b:                                   0.00
>
> work_syevx:                                         1.00
>                         level_shift
> [a.u.]:                                 0.00
>                         smear
> [a.u.]:                                       0.00
>                         added
> MOs                                         0    0
>
> --------------------------------------------------------
>                         Outer loop SCF in use
>                         No variables optimised in outer loop
>
> eps_scf                                         1.00E-05
>
> max_scf                                                5
>                         No outer loop optimization
>
> step_size                                       5.00E-01
>
>  2D_MC| Monte Carlo annealing to optimize the distribution_2d
>  2D_MC| Number of
> moves                                                   400000
>  2D_MC| Number of annealing
> cycles                                            10
>  2D_MC| Number of reduction steps per
> cycle                                    5
>  2D_MC| Reduction factor per step
> 0.8000000000
>  2D_MC| Termination tolerance
> 0.0200000000
>  2D_MC| Maximum temperature
> 0.5000000000
>  2D_MC| Swap probability
> 0.9000000000
>  2D_MC| Number of processor
> rows                                               4
>  2D_MC| Number of processor
> cols                                               4
>  2D_MC| Number of
> elements                                                   150
>  2D_MC| Cost of optimal
> distribution                                      172157
>  2D_MC| Cost of found
> distribution                                        174861
>  2D_MC| Difference in
> percent                                                  2
>
>   Number of electrons:               414
>   Number of occupied orbitals:       207
>   Number of orbital functions:      2338
>
>   Number of independent orbital functions:      2338
>
>   Extrapolation method: initial_guess
>
>
>  SCF WAVEFUNCTION OPTIMIZATION
>
>   Step  Update method              Time         Convergence
> Total energy
>
> ---------------------------------------------------------------------- 
> -------
>
>   ----------------------------------- OT
> --------------------------------------
>
>   Allowing for rotations:  F
>   minimizer      : CG                  : conjugate gradient
>   preconditioner : FULL_SINGLE_INVERSE : cholesky inversion of H + eS
>   line search    : 2PNT                : 2 energies, one gradient
>   stepsize       :    0.15000000
>   energy_gap     :    0.20000000
>   eps_taylor     :   0.10000E-15
>   max_taylor     :             4
>
>   ----------------------------------- OT
> --------------------------------------
>  CP2K| condition FAILED at line 1472
>  CP2K| Abnormal program termination, stopped by process number 13
>  CP2K| condition FAILED at line 1472
>  CP2K| Abnormal program termination, stopped by process number 14
>  CP2K| condition FAILED at line 1472
>  CP2K| Abnormal program termination, stopped by process number 12
>  CP2K| condition FAILED at line 1459
>  CP2K| Abnormal program termination, stopped by process number 8
>  CP2K| condition FAILED at line 1472
>  CP2K| Abnormal program termination, stopped by process number 9
>  CP2K| condition FAILED at line 1472
>  CP2K| Abnormal program termination, stopped by process number 7
>  CP2K| condition FAILED at line 1472
>  CP2K| Abnormal program termination, stopped by process number 4
>  CP2K| condition FAILED at line 1472
>  CP2K| Abnormal program termination, stopped by process number 6
>  CP2K| condition FAILED at line 1472
>  CP2K| Abnormal program termination, stopped by process number 1
>  CP2K| condition FAILED at line 1472
>  CP2K| Abnormal program termination, stopped by process number 3
>  CP2K| condition FAILED at line 1472
>  CP2K| Abnormal program termination, stopped by process number 2
> 7 processes killed (possibly by Open MPI)
> Job  /cineca/sysprod/lsf/7.0/linux2.6-glibc2.3-x86_64/bin/
> openmpi_wrapper ./cp2k.popt prot_6_2103.inp
>
>
> >




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